[gmx-users] force evaluation
Berk Hess
gmx3 at hotmail.com
Tue Jan 6 20:20:40 CET 2009
Hi,
There could be several issues here.
I don't know how you treat the real space cut-off.
Could you be seeing charge groups issues?
You should make sure that each charge group consists of a single atom.
Berk
> Date: Tue, 6 Jan 2009 18:01:16 +0100
> From: dommert at fias.uni-frankfurt.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] force evaluation
>
> * Berk Hess <gmx3 at hotmail.com> [2009-01-06 17:00:06 +0100]:
>
> >
> >Hi,
> >
> >I don't understand what the exact difference is you are referring to.
> >In Gromacs the direct space part for Ewald and PME uses identical
> >code with identical input.
>
> Hello,
>
> sorry I forgot to mention that we have a tool that calculates the
> electrostatic interaction with the Ewald method and the SPME algorithm.
> From this program I get a reference force that can be tuned to a
> certain precision, since Kolaffa and Perram have already
> investigated the error introduced by the Ewald summation. This yields
> as a reference force. Here arises the first problem:
> If I use the same parameters and the Ewald summation the forces in
> gromacs and our tool differ in about 10^-4. That should not be since
> the forces should be exact up to 10^-12.
> A further problem comes up when comparing forces derived with a very
> small splitting parameter beta. This means the error stems from the
> direct part. However the error estimate of Kolaffa and Perram fails for
> the forces calculated by gromacs. The force deviation calculated with our tool
> fits to the estimate, so our code seems to be correct.
>
> Cheers,
> Flo
>
> >So or both Ewald and PME are right or both are wrong.
> >
> >Berk
> >
> >> Date: Tue, 6 Jan 2009 16:33:40 +0100
> >> From: dommert at fias.uni-frankfurt.de
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] force evaluation
> >>
> >> * Berk Hess <gmx3 at hotmail.com> [2009-01-06 15:39:41 +0100]:
> >>
> >> >
> >> >Hi,
> >> >
> >> >The error should not be in the tables, if you are using Gromacs 4.
> >> >We made sure that the accuracy of the tabulation and interpolation
> >> >is nearly the full precision (both in single and double precision).
> >> >
> >> >For these kind of testing purposes you should be using double precision
> >> >anyhow, which gives you far more accuracy than 10^-4.
> >>
> >> Hello,
> >>
> >> of course Gromacs 4 compiled with double precision is used and I even
> >> get a better agreement with my reference force, if the coulomb forces
> >> are tabulated.
> >>
> >> However where could the difference arise ?
> >>
> >> I also tried a version without the software implementation of the invsqrt but it
> >> doesnt change. If our results would not conincide with the error
> >> estimate of Perram and Kolafa, I would say we have a bug in our code.
> >> However the estimate is perfect and that for all cases:
> >> * Ewald Sum (implemented in Gromacs)
> >> * sPME with analytical differentiation (implemented in Gromacs)
> >> * sPME with ik-differentiation
> >>
> >> Cheers,
> >>
> >> Flo
> >>
> >> >
> >> >Berk
> >> >
> >> >> Date: Tue, 6 Jan 2009 14:24:17 +0100
> >> >> From: dommert at fias.uni-frankfurt.de
> >> >> To: gmx-users at gromacs.org
> >> >> Subject: Re: [gmx-users] force evaluation
> >> >>
> >> >> * Mark Abraham <Mark.Abraham at anu.edu.au> [2009-01-07 00:13:00 +1100]:
> >> >>
> >> >> > Suman Chakrabarty wrote:
> >> >> >> On Tue, Jan 6, 2009 at 2:29 PM, Florian Dommert
> >> >> >> <dommert at fias.uni-frankfurt.de> wrote:
> >> >> >>> Finally it would be very interested in a possiblity to switch off the
> >> >> >>> vdw interactions easily. So far I used an appropiate topology files with
> >> >> >>> C6
> >> >> >>> and
> >> >> >>> C12 set to zero. Is there an easier solution as using a table filled
> >> >> >>> with zeros ?
> >> >> >
> >> >> > Zeroed tables will be considerably slower than zeroed parameters.
> >> >> >
> >> >> > Depending on the way the force field is organized, you might create a
> >> >> > version of the force field files that zeroes out these parameters. Another
> >> >> > possibility might be to using the preprocessor mechanism to define the VDW
> >> >> > parameters only under some circumstances.
> >> >>
> >> >> Thank you very much for the help. It seems I went the a good way with
> >> >> using a preprocessing command to define the zero VDW IA.
> >> >>
> >> >> Now I have to find where the difference in the calculation of the
> >> >> electrostatic forces. Perhaps somebody can tell me, where the forces get
> >> >> tabulated, that I can take a look at the code there ?
> >> >>
> >> >> Cheers,
> >> >>
> >> >> Flo
> >> >>
> >> >>
> >> >> >
> >> >> > Mark
> >> >> > _______________________________________________
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> >> >>
> >> >> --
> >> >> Florian Dommert
> >> >> Dipl.-Phys.
> >> >>
> >> >> Computational and Theoretical Softmatter & Biophysics group
> >> >>
> >> >> Frankfurt Institute for Advanced Studies
> >> >> Johann-Wolfgang-Goethe University
> >> >>
> >> >> Ruth-Moufang-Str. 1
> >> >> 60438 Frankfurt am Main
> >> >>
> >> >> Phone: +49(0)69 / 798 - 47529
> >> >> Fax: +49(0)69 / 798 - 47611
> >> >>
> >> >> EMail: dommert at fias.uni-frankfurt.de
> >> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
> >> >
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> >>
> >> --
> >> Florian Dommert
> >> Dipl.-Phys.
> >>
> >> Computational and Theoretical Softmatter & Biophysics group
> >>
> >> Frankfurt Institute for Advanced Studies
> >> Johann-Wolfgang-Goethe University
> >>
> >> Ruth-Moufang-Str. 1
> >> 60438 Frankfurt am Main
> >>
> >> Phone: +49(0)69 / 798 - 47529
> >> Fax: +49(0)69 / 798 - 47611
> >>
> >> EMail: dommert at fias.uni-frankfurt.de
> >> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
> >
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>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Computational and Theoretical Softmatter & Biophysics group
>
> Frankfurt Institute for Advanced Studies
> Johann-Wolfgang-Goethe University
>
> Ruth-Moufang-Str. 1
> 60438 Frankfurt am Main
>
> Phone: +49(0)69 / 798 - 47529
> Fax: +49(0)69 / 798 - 47611
>
> EMail: dommert at fias.uni-frankfurt.de
> Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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